A comprehensive survey of integron-associated genes present in metagenomes

M Buongermino Pereira, T Österlund, KM Eriksson… - BMC genomics, 2020 - Springer
Background Integrons are genomic elements that mediate horizontal gene transfer by
inserting and removing genetic material using site-specific recombination. Integrons are …

Baseline human gut microbiota profile in healthy people and standard reporting template

CH King, H Desai, AC Sylvetsky, J LoTempio… - PloS one, 2019 - journals.plos.org
A comprehensive knowledge of the types and ratios of microbes that inhabit the healthy
human gut is necessary before any kind of pre-clinical or clinical study can be performed …

Discovery of novel bacterial toxins by genomics and computational biology

AC Doxey, MJ Mansfield, C Montecucco - Toxicon, 2018 - Elsevier
Hundreds and hundreds of bacterial protein toxins are presently known. Traditionally, toxin
identification begins with pathological studies of bacterial infectious disease. Following …

Deep embedding and alignment of protein sequences

F Llinares-López, Q Berthet, M Blondel, O Teboul… - Nature …, 2023 - nature.com
Protein sequence alignment is a key component of most bioinformatics pipelines to study the
structures and functions of proteins. Aligning highly divergent sequences remains, however …

An assessment of genome annotation coverage across the bacterial tree of life

B Lobb, BJM Tremblay… - Microbial …, 2020 - microbiologyresearch.org
Although gene-finding in bacterial genomes is relatively straightforward, the automated
assignment of gene function is still challenging, resulting in a vast quantity of hypothetical …

A molecular portrait of de novo genes in yeasts

N Vakirlis, AS Hebert, DA Opulente… - Molecular biology …, 2018 - academic.oup.com
New genes, with novel protein functions, can evolve “from scratch” out of intergenic
sequences. These de novo genes can integrate the cell's genetic network and drive …

Unifying the known and unknown microbial coding sequence space

C Vanni, MS Schechter, SG Acinas, A Barberán… - Elife, 2022 - elifesciences.org
Genes of unknown function are among the biggest challenges in molecular biology,
especially in microbial systems, where 40–60% of the predicted genes are unknown …

Microbial dark matter investigations: how microbial studies transform biological knowledge and empirically sketch a logic of scientific discovery

G Bernard, JS Pathmanathan, R Lannes… - Genome biology and …, 2018 - academic.oup.com
Microbes are the oldest and most widespread, phylogenetically and metabolically diverse
life forms on Earth. However, they have been discovered only 334 years ago, and their …

Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins

N Vakirlis, A Kupczok - Genome Research, 2024 - genome.cshlp.org
Species-specific genes, also known as orphans, are ubiquitous across life's domains. In
prokaryotes, species-specific orphan genes (SSOGs) are mostly thought to originate in …

Discovering novel hydrolases from hot environments

R Wohlgemuth, J Littlechild, D Monti, K Schnorr… - Biotechnology …, 2018 - Elsevier
Novel hydrolases from hot and other extreme environments showing appropriate
performance and/or novel functionalities and new approaches for their systematic screening …